@@ -106,7 +106,10 @@ hasBiomartConnection <- (!is(try(download.file("http://www.biomart.org", tempfil

                          !is(try(biomaRt::listMarts(), silent=TRUE), "try-error"))

 options(timeout=oto)

-## Uncommenting this helps when the UCSC server has a hickup but still lets you connect:

+## ## clear BiomaRt cache

+## biomaRt::biomartCacheClear()

+

+## ## Uncommenting this helps when the UCSC server has a hickup but still lets you connect:

 ## hasUcscConnection <- !is(try(rtracklayer::browserSession(), silent=TRUE), "try-error") && 

 ##   !is(try(IdeogramTrack(genome="hg19", chromosome=7), silent=TRUE), "try-error")

 ```

@@ -942,22 +945,21 @@ set is plotted for the horizon type for the sake of clarity.]

 ```{r typeGroupedPlots, fig.width=7.5, fig.height=6, echo=FALSE, results='hide'}

 pushViewport(viewport(layout=grid.layout(nrow=9, ncol=1)))

 i <- 1

-for(t in c("a", "s", "confint", "smooth", "histogram", "boxplot", "heatmap", "horizon")) {

-    pushViewport(viewport(layout.pos.col=((i-1)%%1)+1, layout.pos.row=((i-1)%/%1)+1))

-    if(t != "horizon") {

-        names(dTrack) <- t

-        plotTracks(dTrack, type=t, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)

-    } else {

-        plotTracks(dtHoriz[c(1,8),], type="horizon", add=TRUE, cex.title=0.8, margin=0.5, showAxis=FALSE, horizon.origin=0.3,

-                   groups=1:2)

-    }

-    i <- i+1

-    popViewport(1)

+for(t in c("a", "s", "confint", "smooth", "histogram", "boxplot", "heatmap", "horizon", "hor. type")) {

+  pushViewport(viewport(layout.pos.col=((i-1)%%1)+1, layout.pos.row=((i-1)%/%1)+1))

+  names(dTrack) <- t

+  if(!t %in% c("horizon", "hor. type")) {

+    plotTracks(dTrack, type=t, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)

+  } else if (t == "horizon") {

+    plotTracks(dtHoriz[c(1,8),], type="horizon", add=TRUE, cex.title=0.8, margin=0.5, showAxis=FALSE, horizon.origin=0.3,

+               groups=1:2)

+  } else {

+    plotTracks(dTrack, type="histogram", stackedBars=FALSE, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)

+  }

+  i <- i+1

+  popViewport(1)

 }

-pushViewport(viewport(layout.pos.col=((i-1)%%1)+1, layout.pos.row=((i-1)%/%1)+1))

-names(dTrack) <- "hor. hist."

-plotTracks(dTrack, type="histogram", stackedBars=FALSE, add=TRUE, cex.title=0.8, groups=rep(1:2, each=3), margin=0.5)

-popViewport(2)

+popViewport(1)

 names(dTrack) <- "uniform"

 ```